Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.7.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06429	0.827
27DAP/17DAP	0.7766	0.35
39DAP/27DAP	1.32069	0.768
41DAP/39DAP	1.69251	0.138
42DAP/41DAP	1.08045	0.992
43DAP/42DAP	1.75757	0.045
47DAP/43DAP	2.33658	0.334
52DAP/47DAP	1.47322	0.466
57DAP/52DAP	1.08355	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00706	1
17DAP/reference	1.09525	0.011
27DAP/reference	1.09279	0.232
39DAP/reference	1.04407	0.359
41DAP/reference	1.15066	0.054
42DAP/reference	0.9915	0.455
43DAP/reference	1.07085	0.142
47DAP/reference	0.99656	0.674
52DAP/reference	0.93209	0.405
57DAP/reference	1.0781	0.344

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.91871	0.484
27DAP/17DAP	1.12844	0.639
39DAP/27DAP	1.6756	0.067
41DAP/39DAP	0.5863	0.037
42DAP/41DAP	2.60805	0.002
43DAP/42DAP	3.32627	0.014
47DAP/43DAP	0.94686	0.87
52DAP/47DAP	1.24318	0.508
57DAP/52DAP	0.94951	0.726
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.63228	0.039
17DAP/reference	0.76261	0.031
27DAP/reference	1.12851	0.107
39DAP/reference	1.60235	0.013
41DAP/reference	1.29511	0.025
42DAP/reference	1.23687	0.132
43DAP/reference	1.27682	0.256
47DAP/reference	1.37831	0.214
52DAP/reference	0.96444	0.435
57DAP/reference	0.71262	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95045	0.669
17DAP/reference	1.04594	0.229
27DAP/reference	0.96017	0.483
39DAP/reference	1.054	0.477
41DAP/reference	0.99021	0.615
42DAP/reference	1.03553	0.81
43DAP/reference	1.20663	0.116
47DAP/reference	0.99274	0.678
52DAP/reference	1.02578	0.747
57DAP/reference	1.09336	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.62722	0.032
17DAP/reference	0.8635	0.308
27DAP/reference	0.78045	0.081
39DAP/reference	0.93574	0.271
41DAP/reference	0.90333	0.293
42DAP/reference	1.59175	0.049
43DAP/reference	1.66221	0.066
47DAP/reference	0.97934	0.538
52DAP/reference	1.51888	0.134
57DAP/reference	1.01757	0.553

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01981	0.966
26DAP/20DAP	0.53357	0.228
34DAP/26DAP	1.17392	0.304
51DAP/34DAP	1.32935
52DAP/51DAP	1.09618	0.808
53DAP/52DAP	1.74989	0.284
55DAP/53DAP	1.32992
57DAP/55DAP	1.05527
62DAP/57DAP	0.38694
68DAP/62DAP	1.02675
68DAP/14DAP	N/A	N/A

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	3.2215	0.016

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	7.71867	0.089
Mature Green Tomato/Ripe Tomato	0.38763	0.132
Immature Eggplant/Mature Eggplant	0.2755	0.062
Ripe Pepper/Ripe Tomato	0.81374	1
Mature Eggplant/Ripe Tomato	2.39442	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01949	0.742
1-1-2/M82	1.26876	1
12-2/M82	1.38958	1
12-4/M82	0.95487	0.619
1-3/M82	0.82335	0.501
2-1-1/M82	0.8721	0.465
2-1/M82	1.0701	1
2-6/M82	0.94308	1
3-2/M82	0.14456
4-1-1/M82	0.95984	1
4-1/M82	1.02113	1
4-3-2/M82	0.9226	1
4-3/M82	0.93564	0.72
5-3/M82	0.87291	1
6-2/M82	1.00228	1
6-3/M82	1.00562	1
7-1/M82	0.95091	0.803
7-2/M82	1.06517	1
9-3-2/M82	1.06658

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	N/A	N/A

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10457	0.894
DC3000/delta hrp 6h	1.26369	1
DC3000/delta hrp 12h	1.06039	1
DC3000/delta hrp 24h	0.87325	0.178

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05068	0.355
DC3000 delta B/DC3000 delta AB	N/A	N/A

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01931	1
Exp 36h	N/A	N/A
Exp 60h	0.39368	0.249

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.06911	1
Var 0h	0.97468	1
Var 12h I row2-row1	1.24157	0.235
Var 12h NI row2-row1	1.01881	1
Var 36h I row2-row1	1.07868	1
Var 36h NI row2-row1	0.90274	0.61
Var 60h I row2-row1	0.70398	0.582
Var 60h NI row2-row1	0.99166	1
Time course 0hI-0hNI	0.95727	0.711
Time course 12hI-12hNI	0.94401	0.628
Time course 36hI-36hNI	0.92229	0.317
Time course 60hI-60hNI	1.39751	0.012

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.79817	0.301
transgenic ySAMdc/azygous control (breaker)	1.13592	1
transgenic ySAMdc/azygous control (red)	1.00429	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98829	0.459

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86012	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.62619	1
Manapal/WT (break)	0.97427	1
Manapal/WT (red)	0.88961	0.274